Literature DB >> 20686882

Molecular dynamics simulation using weak-coupling NOE distance restraining.

A P Nanzer1, T Huber, A E Torda, W F van Gunsteren.   

Abstract

Application of the weak-coupling scheme to restrain the configurations of a molecular system to a set of NOE distance restraints is investigated using two test systems: (i) a 15-atom chain molecule with one distance restraint; and (ii) a protein molecule with hundreds of NOE distance restraints. Atom-atom distance restraining by the weak-coupling technique is possible, but this method does not produce as good results as the penalty function method normally used to maintain NOE distance restraints.

Year:  1996        PMID： 20686882     DOI： 10.1007/BF00410327

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  13 in total

1.  Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

Authors:  A E Torda; R M Scheek; W F van Gunsteren
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

2.  A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.

Authors:  A P Nanzer; F M Poulsen; W F van Gunsteren; A E Torda
Journal:  Biochemistry       Date:  1994-12-06       Impact factor: 3.162

3.  Parametrisation of time-averaged distance restraints in MD simulations.

Authors:  A P Nanzer; W F van Gunsteren; A E Torda
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

4.  How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

5.  The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics.

Authors:  G M Clore; A M Gronenborn; M Kjaer; F M Poulsen
Journal:  Protein Eng       Date:  1987 Aug-Sep

6.  Structure refinement using time-averaged J-coupling constant restraints.

Authors:  A E Torda; R M Brunne; T Huber; H Kessler; W F van Gunsteren
Journal:  J Biomol NMR       Date:  1993-01       Impact factor: 2.835

7.  Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data.

Authors:  U Schmitz; N B Ulyanov; A Kumar; T L James
Journal:  J Mol Biol       Date:  1993-11-20       Impact factor: 5.469

8.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

Authors:  R Kaptein; E R Zuiderweg; R M Scheek; R Boelens; W F van Gunsteren
Journal:  J Mol Biol       Date:  1985-03-05       Impact factor: 5.469

9.  Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.

Authors:  K Wüthrich; M Billeter; W Braun
Journal:  J Mol Biol       Date:  1983-10-05       Impact factor: 5.469

10.  Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of phi-angles.

Authors:  S Ludvigsen; K V Andersen; F M Poulsen
Journal:  J Mol Biol       Date:  1991-02-20       Impact factor: 5.469
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  2 in total

1.  Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

Authors:  Jozica Dolenc; John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2010-06-04       Impact factor: 2.835

Review 2.  Hybrid methods for combined experimental and computational determination of protein structure.

Authors:  Justin T Seffernick; Steffen Lindert
Journal:  J Chem Phys       Date:  2020-12-28       Impact factor: 3.488
  2 in total

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